3HTG

2-ethoxy-3,4-dihydro-2h-pyran in complex with T4 lysozyme L99A/M102Q


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1LGUPDB ENTRY 1LGU

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.52772.2M sodium-potassium phosphate, 0.05M beta-mercaptoethanol, 0.05M 2-hydroxyethyldisulfide, pH 6.5, vapor diffusion, hanging drop, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.754.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 60.11α = 90
b = 60.11β = 90
c = 96.44γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray296CCDADSC QUANTUM 315r2008-01-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.3.11.11589ALS8.3.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.253095.30.06515.466.295381453814
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.251.3376.70.2574.84.93

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONREFMACTHROUGHOUTPDB ENTRY 1LGU1.2627.35538125273510771000.164830.16450.18101RANDOM12.662
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
0.220.110.22-0.33
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.026
r_dihedral_angle_3_deg10.69
r_dihedral_angle_4_deg10.309
r_dihedral_angle_1_deg4.704
r_sphericity_free3.095
r_sphericity_bonded2.388
r_scangle_it2.262
r_scbond_it1.705
r_mcangle_it1.204
r_angle_refined_deg1.168
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.026
r_dihedral_angle_3_deg10.69
r_dihedral_angle_4_deg10.309
r_dihedral_angle_1_deg4.704
r_sphericity_free3.095
r_sphericity_bonded2.388
r_scangle_it2.262
r_scbond_it1.705
r_mcangle_it1.204
r_angle_refined_deg1.168
r_rigid_bond_restr0.917
r_mcbond_it0.81
r_nbtor_refined0.311
r_symmetry_vdw_refined0.205
r_nbd_refined0.191
r_xyhbond_nbd_refined0.16
r_symmetry_hbond_refined0.134
r_chiral_restr0.08
r_bond_refined_d0.007
r_gen_planes_refined0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1375
Nucleic Acid Atoms
Solvent Atoms320
Heterogen Atoms18

Software

Software
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
XDSdata reduction
XDSdata scaling
REFMACphasing